rs2158177

Variant names:

• chr5-132648366-A-G
• rs2158177
• ENST00000458509.1:n.105-6084T>C

Your query was ambiguous. Multiple possible variants found:

• chr5-132648366-A-G
• chr5-132648366-A-T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000458509.1(TH2LCRR):​n.105-6084T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.177 in 152,202 control chromosomes in the GnomAD database, including 2,539 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.18 (2539 hom., cov: 32)
• Consequence: TH2LCRR ENST00000458509.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.461
• Publications: 28 publications found

Genes affected

TH2LCRR (HGNC:40495): (T helper type 2 locus control region associated RNA)

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.74).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.203 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000458509.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	TH2LCRR	NR_132125.1		n.105-6084T>C		intron	N/A
	TH2LCRR	NR_132126.1		n.174+7353T>C		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	TH2LCRR	ENST00000458509.1	TSL:1	n.105-6084T>C		intron	N/A
	TH2LCRR	ENST00000417516.2	TSL:2	n.474+7353T>C		intron	N/A
	TH2LCRR	ENST00000435042.1	TSL:5	n.95-6084T>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.177 AC: 26960 AN: 152084 Hom.: 2536 Cov.: 32

Gnomad AFR AF: 0.124

Gnomad AMI AF: 0.122

Gnomad AMR AF: 0.139

Gnomad ASJ AF: 0.220

Gnomad EAS AF: 0.176

Gnomad SAS AF: 0.214

Gnomad FIN AF: 0.233

Gnomad MID AF: 0.241

Gnomad NFE AF: 0.205

Gnomad OTH AF: 0.185

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.177 AC: 26977 AN: 152202 Hom.: 2539 Cov.: 32 AF XY: 0.179 AC XY: 13304 AN XY: 74400

African (AFR) AF: 0.124 AC: 5143 AN: 41542

American (AMR) AF: 0.139 AC: 2123 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.220 AC: 762 AN: 3470

East Asian (EAS) AF: 0.177 AC: 916 AN: 5184

South Asian (SAS) AF: 0.214 AC: 1034 AN: 4826

European-Finnish (FIN) AF: 0.233 AC: 2466 AN: 10578

Middle Eastern (MID) AF: 0.241 AC: 71 AN: 294

European-Non Finnish (NFE) AF: 0.205 AC: 13965 AN: 67992

Other (OTH) AF: 0.183 AC: 386 AN: 2112

Alfa AF: 0.190 Hom.: 531

Bravo AF: 0.165

Asia WGS AF: 0.186 AC: 649 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.74
CADD	Benign	3.0
DANN	Benign	0.76
PhyloP100		0.46
Mutation Taster		=100/0	polymorphism

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs2158177;

hg19: chr5-131984058;